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BACKGROUND: Despite its clinical effectiveness, allergen immunotherapy (AIT) remains controversial because serious systemic reactions can occur during its administration. Most of the studies on the safety of AIT are retrospective and use different methods, which frequently depart from daily clinical practice. OBJECTIVE: The aim of this study was to determine risk factors for adverse reactions, especially systemic adverse reactions, produced during routine AIT administration. METHODS: We registered 5,768 consecutive doses of standardized extracts administered to 273 patients in conventional schedules, following the recommendations on safety and data collection of the European Academy of Allergology and Clinical Immunology. Of the 273 patients, 236 were asthmatics, 28 had rhinitis and 9 received immunotherapy due to Hymenoptera anaphylaxis. RESULTS: We examined 143 local reactions (2.48 % of the doses) and 145 systemic reactions (78 immediate and 67 delayed). Risk factors for developing an immediate systemic reaction were asthma severity, sensitization to molds, the most concentrated vials and a fall in peak expiratory flow of more than 15 % or an immediate systemic reaction in the previous dose. Late systemic reactions were significantly more frequent with less concentrated vials and in patients with late local reactions in the previous dose. No serious reactions were registered. CONCLUSIONS: We believe that AIT is reliable when used with strict safety protocols and administered by specialized staff. Risk factors for adverse reactions to this type of treatment can be identified and reduced by systematic data collection.